I want to use json ld micro-data from schema.org to reference images on my website but at the same time retrieve the json ld object in my Javascript to use it for others things. The problem is that I want to add custom fields that do not match any type in Schema.org. My question is, will search engines just ignore the fields they don't recognize or discard the whole micro-data ?
Short answer, yes they’ll ignore properties they don’t define, and it’s quite normal to use JSON-LD for other purposes, such as to drive your UI. That said, it’s best if these properties and types come from a known vocabulary, or even resolve to your own. It’s always good to test your data patterns first, using any of the online tools available.
Also, it’s not JSON-LD micro-data, they are actually two different things, both of which (along with RDFa) can be used to provide schema.org markup. JSON-LD is contained in a script element, the others are expressed using HTML attributes.